The small-fruit phenotypes were controlled by nine major-effect loci with complementary epistasis in Malus accessions

Abstract

During the long history of domestication and improvement of cultivated plants from their wild progenitors, unfavorable alleles of important traits, such as the small-fruit trait of wild apple (Malus) species, have undergone gradual negative selection. Utilizing wild species as breeding materials for elite lines requires removing these undesirable alleles, making it urgent to identify these allelic variations. We previously identified 90 quantitative trait loci (QTLs) for apple fruit weight via bulked segregant analysis-seq. In this study, we identified 37 genome regions associated with apple fruit weight by genome-wide association study (GWAS) using 253 Malus accessions. We then developed 147 GenoBaits markers within the QTL intervals or association regions, of which nine were major-effect markers for small-fruit traits and exhibited complementary epistasis. Nineteen candidate genes were predicted within the nine major-effect loci. Overexpressing three of these genes, MdPMEI51, MdTIP1-1, and MdARF9, inhibited cell proliferation in transgenic apple calli, and allelic variants in their coding sequences enhanced these inhibitory effects. We replaced the nearby linkage marker with MdTIP1-1 SNP700 A/G (Chr12_16 957 078 T/C, on the antisense strand) and identified seven markers as major-effect markers for the large-fruit trait. We added the joint effects of the nine and seven major-effect markers for the small- and large-fruit phenotypes, respectively, to genomics-assisted prediction (GAP) models as fixed effects. The prediction accuracy of the non-additive GAP model was 0.8436. The frequency of the small-fruit associated alleles of the nine major-effect markers is much higher in wild Malus species than in cultivated and semi-cultivated species, indicating that the alleles associated with the small-fruit trait underwent strong negative selection during domestication. These findings shed light on the genetic mechanism underlying the small-fruit trait in apple and could facilitate apple breeding.